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Early Career Faculty Training Notes
Attendance (Katz): Shawn Bowers, Dan Higgins, Samantha Katz, Bill Michener, Deana Pennington, Mark Schildhauer, Aimee Stewart, David Thau
Goals for this training to have users return from training and be able to:
- Create a scientific workflow before they start in kepler. This is something that can help organize their thought process of conducting research. This workflow could and we should then be created in kepler
- Use their own dataset in a pre-existing kepler workflow
- Create their own simple kepler workflow using r.
- Enter their own data using either morpho and the knb data registry and get that data into a kepler workflow -- a simple exercise that exploits
- Show how kepler utilizes the EcoGrid and how that functions into the importance of well structured data sets and databases -- which includes QA/QC
- Show how kepler utilizes the functionalities of KR SMS -- how the semantic, semantic mediation and annotation through ontologies works for them and how this is linked to well documented and well structured datasets.
- Show how taxonomic resolution works and how this is linked to well documented and well structured datasets.
Review agenda
Discussion on linking the training together with the same dataset used throughout the training
- update presentation with the common dataset;
- Deana will send out npp dataset
- link Dan Higgins presentation on r with Kristin's presentation on QA/QC -- Dan will try to illustrate some of the approaches Kristin covers in her presentation -- share screenshots Sam will send email Dan the QAQC presentation and email Kristin and Dan to facilitate
- Grid activity -- provide example that illustrates the distributed execution notion and link back to Kepler and how that is executed. Will and Mark will work on this
- Will's presentation on Eml and morpho link link to Grid presentation and tie into Dan's presentation on Kepler.
- Visualization in Kepler (demo + exercise) -- will cover a summary of the r, image j -- raster type and photoshop -- pdfs : tables; images; time series example show them the examples in kepler imaging Dan and Deana will work on this
- Taxonomic resolution in Kepler –Stewart -- will cover GBIF; Biota; query into DIGIR and IT IS, Vegbank demo Sam will work with Aimee on presentation
- KR SMS presentation by Shawn will close up the week by revisitng topics covered previously during the week: the importance of well documented and well structured datasets and how this is exploited through semantic mediation and ontologies. Using an exercise that illustrates problems of and solutions to data integration.
Documentation Notes
Attendance (Katz): Laura Downey, Dan Higgins, Samantha Katz, Deana Pennington, Mark Schildhauer
Review Getting Started Guide documentation for the release
- First example -- Simple Addition changed to Simple Statistics -- needs reviewed for edits and completeness -- Need Dan to review and save as workflow for the Beta3 release
- Need to finish updating section 5.3 Director and Actor Icons with most recent icon family categories for the Beta3 release. Sam used the 3 "all-the-actors actor in workflows" directory that Matt made and went back to svg and made some adaptation to create an initial list. Laura needs to be reviewed and make suggestion
- Need to finish the screenshots in the GSG. Need to go over the graphic designers images with Laura
- Need to change the default parameter in Lotka-Volterra model for the GSG and the saved workflows
- Need to identify channels in the images -- make sure this is reflected in the document and that we adequately describe channel and this idea.
- Need to add a list in the GSG about the complete list of workflows that are shipped with the release
- Need to add a note/table about workflows and the difference between the nightly build and the release and the
- Adding director and extra r workflows? Should we just keep expanding the GSG?
Review actor classifications
- List of list SEEK actors and workflows -- make sure these lists correspond
- Review and request developer level actor documentation -- need help Dan, Ilkay and Efrat cannot be the only people reviewing It was decided that we would only create user level documentation for those actors that: related to the SEEK project; has adequate developer documentation; or the developer was willing to work with us.
- Removed the following actors from the actor documentation: File to String Converter ; Invoke server; ServerExecute, TempActor. The list of actors will be reviewed and extended based upon a review by Dan, Samantha and Kirsten
- Naming convention -- camel case conventions
- Incorporating documentation into application. work with David Sledge on an alternative strategy to the "cut and paste method."
KR- SMS ontology
- What kind of documentation is needed? Why? ask laura for appendices and one-page description
FAQ needs to be expanded to include the following
- Native windows “zip” doesn’t work for Kepler
- Link to GSG
- deletion of kepler cache and note about deleting cache removes any remote components.
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